OpenMS
MassFeatureTrace.h
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1 // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Kyowon Jeong, Jihyung Kim $
6 // $Authors: Kyowon Jeong, Jihyung Kim $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
16 #include <iomanip>
17 #include <iostream>
18 
19 namespace OpenMS
20 {
32  class OPENMS_DLLAPI MassFeatureTrace : public DefaultParamHandler
33  {
34  public:
37 
40 
42  ~MassFeatureTrace() override = default;
43 
46 
48  MassFeatureTrace(MassFeatureTrace&& other) = default;
49 
53 
56 
61  std::vector<FLASHDeconvHelperStructs::MassFeature> findFeatures(const PrecalculatedAveragine& averagine);
62 
63  protected:
64  void updateMembers_() override;
65 
66  private:
70  std::map<double, std::map<double, PeakGroup>> peak_group_map_; // rt , mono mass, peakgroup
71  };
72 } // namespace OpenMS
A class representing a deconvolved spectrum. DeconvolvedSpectrum consists of PeakGroups representing ...
Definition: DeconvolvedSpectrum.h:30
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
log transformed peak. After deconvolution, all necessary information from deconvolution such as charg...
Definition: FLASHDeconvHelperStructs.h:139
Averagine patterns pre-calculated for speed up. Other variables are also calculated for fast cosine c...
Definition: FLASHDeconvHelperStructs.h:34
Feature trace in mass dimension for FLASHDeconv This class performs mass tracing on the deconvolved m...
Definition: MassFeatureTrace.h:33
MassFeatureTrace(const MassFeatureTrace &)=default
copy constructor
FLASHDeconvHelperStructs::LogMzPeak LogMzPeak
Definition: MassFeatureTrace.h:36
~MassFeatureTrace() override=default
destructor
MassFeatureTrace & operator=(const MassFeatureTrace &fd)=default
assignment operator
MassFeatureTrace & operator=(MassFeatureTrace &&fd)=default
void storeInformationFromDeconvolvedSpectrum(DeconvolvedSpectrum &deconvolved_spectrum)
Obtain and store information from deconvolved_spectrum (necessary information for mass tracing afterw...
std::map< double, std::map< double, PeakGroup > > peak_group_map_
peak group information is stored in here for tracing
Definition: MassFeatureTrace.h:70
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
std::vector< FLASHDeconvHelperStructs::MassFeature > findFeatures(const PrecalculatedAveragine &averagine)
Find mass features.
MassFeatureTrace()
constructor
MassFeatureTrace(MassFeatureTrace &&other)=default
move constructor
FLASHDeconvHelperStructs::PrecalculatedAveragine PrecalculatedAveragine
Definition: MassFeatureTrace.h:35
double min_isotope_cosine_
cosine thresholds for scoring and filtering
Definition: MassFeatureTrace.h:68
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19